Write Apple ProRes files from Blender?
It is likely wiser to adopt an image based pipeline and assert that all of your color transforms and bit fidelity remain intact.
Using an image as an intermediate will be vastly more effective. The granularity required to handle the color primaries, bit depth, and transfer curve out of a codec correctly is not currently possible within Blender nor many other mainstream applications, and will often result in incorrect output. Well documented issues such as Quicktime's perceptual noise addition, incorrect transfer curve / gamma, inconsistent vendor flag reading, etc. all make for the stuff of nightmare when dealing with codecs.
If you are careful, you can easily step to an intermediate image format and use the Baptiste Coudurier FFMBC project to encode and decode ProRes with much more control, quality, and accuracy.
While it is a fork of FFMPEG, FFMBC extends the needs of the encoding and decoding of ProRes and DNxHD to meet media broadcast needs.
Further links:

https://code.google.com/p/ffmbc/